The regulation of gene transcription is critical for the development of multi-cellular organisms and aberrations in transcriptional regulation are frequently associated with disease. The regulation of transcription involves cis-regulatory DNA sequences that interact with DNA-binding transcription factors and integrate information that is communicated to the promoter to control the synthesis of mRNA transcripts by RNA polymerase. Cis-regulatory elements in eukaryotes can be located upstream, downstream, or even within the transcribed region of a gene, and in animal systems extending from fruit fly to man are frequently many kilobases removed from the transcription start site. The expression of genes in different cell types at different stages of development is reflected by the occurrence of multiple cis-regulatory elements, each of which interacts with different sets of transcription factors to integrate the control signals that eventually result in gene transcription. Although interactions between different cis-elements and the transcription unit are central to this strategy of controlling gene expression, there is as of yet no clear understanding of how enhancer-promoter interactions are regulated. The tools available in the Drosophila system in conjunction with the framework of knowledge on the pathway responsible for generating the segmented body pattern of the early embryo provide a valuable model for investigating the in vivo mechanisms of transcription regulation. A key player in the segmentation pathway is Runt, the founding member of a family of transcriptional regulators with wide-ranging roles in animal development and human disease. The work in this proposal emanates from studies on sloppy-paired-1 (slp1), a target of Runt in the segmentation pathway that offers numerous advantages for dissecting transcriptional control mechanisms. The initial metameric expression of slp1 is generated in response to a simple combinatorial code that is mediated by two distinct cis-elements. Importantly, the two elements together generate a pattern beyond what is expected from the additive combination of their independent patterns. A model accounting for the functional interplay between these elements proposes a novel role for Runt in regulating interactions between these two elements and the slp1 promoter. The proposed work further investigates the molecular basis for this regulatory phenomenon and includes experiments asking whether a similar regulation of enhancer-promoter interactions contributes to the expression of other genes in the early embryo. The results will provide new insights on the mechanisms of regulation by Runt and other transcription factors that are likely to have widespread implications for understanding the roles of related proteins in human development and disease.